Current earth observation models do not take into account the influence of water salinity on the evaporation rate, even though the salinity influences the evaporation rate by affecting the density and latent heat of vaporization. In this paper, we adapt the SEBS (Surface Energy Balance System) model for large water bodies and add the effect of water salinity to the evaporation rate. Firstly, SEBS is modified for fresh-water whereby new parameterizations of the water heat flux and sensible heat flux are suggested. This is achieved by adapting the roughness heights for momentum and heat transfer. Secondly, a salinity correction factor is integrated into the adapted model. Eddy covariance measurements over Lake IJsselmeer (The Netherlands) are carried out and used to estimate the roughness heights for momentum (~0.0002 m) and heat transfer (~0.0001 m). Application of these values over the Victoria and Tana lakes (freshwater) in Africa showed that the calculated latent heat fluxes agree well with the measurements. The root mean-square of relative-errors (rRMSE) is about 4.1% for Lake Victoria and 4.7%, for Lake Tana. Verification with ECMWF data showed that the salinity reduced the evaporation at varying levels by up to 27% in the Great Salt Lake and by 1% for open ocean. Our results show the importance of salinity to the evaporation rate and the suitability of the adapted-SEBS model (AquaSEBS) for fresh and saline waters.